Resource from Got Questions? at http://www.gotquestions.org/about.html
The issue is not whether we should question God, but in what manner—and for what reason—we question Him. To question God (to ask question for an answer) is not in itself wrong. The prophet Habakkuk had questions for God concerning the timing and agency of the Lord’s plan. Habakkuk, rather than being rebuked for his questions, is patiently answered, and the prophet ends his book with a song of praise to the Lord. Many questions are put to God in the Psalms (Psalms 10, 44, 74, 77). These are the cries of the persecuted that are desperate for God’s intervention and salvation.
Although God does not always answer our questions in the way we want, we conclude from these passages that a sincere question from an earnest heart is welcomed by God as He desires a close trusting relationship with Him. We question out of the sincere heart to understand and know God, not out of a distrustful and disbelief heart to doubt God.
Insincere questions, or questions from a hypocritical heart, are a different matter. “And without faith it is impossible to please God, because anyone who comes to him must believe that he exists and that he rewards those who earnestly seek him” (Hebrews 11:6). After King Saul had disobeyed God, his questions went unanswered (1 Samuel 28:6). It is entirely different to wonder why God allowed a certain event than it is to directly question God's action or goodness. Having sincere doubt is different from questioning God's sovereignty and attacking His character.
In short, an honest question is not a sin, but a bitter, untrusting, or rebellious heart is. God is not intimidated by questions. God invites us to enjoy close fellowship with Him and He allows us the progress of growing in knowing Him through time and experience. When we “question God,” it should be from a humble spirit and open mind to know, not to doubt with discontentment or rebelliously dissatisfied at God. We can question God, but we should not expect an answer unless we are genuinely interested in His answer. God knows our hearts, and knows whether we are genuinely seeking Him to enlighten us or not. Our heart attitude is what determines whether it is right or wrong to question God.
